A fox of the same species was found in a much older grave in another part of Argentina nearly a decade ago. It may also have been a pet but its diet was not analysed.
It's much more about the specific burial and the inferences that can be reasonably drawn about South America before the introduction of dogs from the north 5k years ago. It references multiple burials with non-dog canids from across time periods in S.A., including at least one from about 4k years ago, as well as many other remains scattered in with human burials. It seems to build on existing theorizing that pre-Columbian practices might have changed more slowly than post. Then there are the statistical arguments. If you occasionally find a fox in human burials, based on the number of human burials you didn't find, you can feel pretty confident that there were more foxes buried with humans.
I did not do a very deep dive but it looks like there were "domesticated" dogs in the Americans prior to Europeans, but they were almost completely replaced by their European counterparts. This leads me to believe the European versions were far superior for the intended usage. If the American version was indeed significantly inferior for their intended purposes, they may have been at or below the effectiveness/usefulness levels of semi-domesticated animals, like foxes.
Edit: The_Sasswagon brings up a good point about the effects of potential European diseases on American dogs.
I don't think that is a safe conclusion at all, the colonial Europeans were pretty notorious for removing anything or anyone or anything they didn't see as civilized in the Americas. They also brought disease that wiped out an astounding number of the native people. From an also uninformed view it would be just as likely the native dogs suffered a similar fate, or simply disbanded and roamed free when their companions died.
That's a good point about disease and I think it could be a potential cause of the low genetic prevalence.
I don't know about your roaming free option. I think if that were true, there would still be wild packs today or there would have been roving dog packs mentioned in historical text (possible but I don't recall any mention of them). Alternatively, they would have inter-breed with European varieties and had a more significant impact on genetics, but that's not seen.
While I agree that Europeans liked to remove/exterminate "uncivilized" things, that mostly applies to people. I suspect if the American dogs were significantly useful they would have made use of them.
This conversation allowed me to recall that the plains tribes utilized dogs as pack animals. Then once horses made their way onto the scene those tribes switched from dogs to horses for that role. I'm not sure what other "jobs" American dogs performed but I suspect if they were significantly utilized as pack animals they were probably breed for such and with that niche gone they may not have performed well in other "dog" tasks, compared to European varieties.
To conclude, for American dogs to be such a small percent of the current dog genome, I think, the European varieties had to significantly outlive their American counterparts. Whether because they were replaced by better performing European varieties/horses, because they died from European diseases, or a combination of those options.
Ha. Yeah estimated at 15,000 years ago. Archeaology often seems presumptious... We found a single fox buried with a human. Ergo: all humans had a fox named Slinky, whom they shared their secrets with in fox tongue language -- those that they could not divuldge to their family, lest they be scorned.